


The Second Stain

by I_am_SHERlocked (SLUG_CAT624), SLUG_CAT624



Category: Sherlock (TV)
Genre: America, Angst, Coping, Crime Scenes, Deductions, Ebola Zaire, Government Conspiracy, Hurt No Comfort, Hurt/Comfort, John and Mary's House, Multi, Music, Off-screen Rape, On-screen Torture, Post-Episode: s04e03 The Final Problem, Post-Traumatic Stress Disorder - PTSD, Soldier Poet King by the Oh Hellos, Spoilers, Under re-write, case!fic, kidnappings, post Serbia, post Sherringford
Language: English
Status: In-Progress
Published: 2019-07-16
Updated: 2020-02-15
Packaged: 2020-06-29 18:44:15
Rating: Mature
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 6
Words: 4,020
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/19836289
Author URL: https://archiveofourown.org/users/SLUG_CAT624/pseuds/I_am_SHERlocked, https://archiveofourown.org/users/SLUG_CAT624/pseuds/SLUG_CAT624
Summary: Formerly titled "The Adventure of the West Wind".In which another erratic genius (and villain) is discovered, everyone is still recovering from Sherrinford, and John and Sherlock have to try and save the world- like the world, world.  Yeah.  Things just got real.





	1. Chapter 1

**Author's Note:**

> This story has not been Britpicked or Beta-read. Please read at your own risk.

##  Previously on SHERLOCK…

“He wanted to kill someone, Mr. ‘Olmes.” Faith grips her cane tightly.

_ “Anyone!” _

Culverton Smith’s face leers out of the television screen, a banner along the bottom proclaiming  _ ‘The hat detective is right! Mass murderer revealed!’ _

The therapist’s house, a frown on her face. “Can’t you guess?”

“I’m Eurus.” 

Eurus dressed in a starch white gown. “Come closer, Sherlock. Be naughty.” 

Sherlock pounds what could have been Molly Hooper’s coffin to bits.

_ “And we’ve reached the end of the line- Holmes killing Holmes.”  _ Sherlock presses the muzzle of the gun to his chin.

“Remember me.” 

Eurus huddled on the floor, and Sherlock’s coat swamping them both. “Eurus, help me save John Watson.”

#  Chapter 1

It’s a blustery fall day at the start of the school year. It’s noon, and the highschool’s courtyard is full with students enjoying the crisp chill after blazing summer skies. A girl grins and waves goodbye to a group of chattering friends at a covered table, and walks crowds of students in the courtyard, making her way for a dejected-looking tree on the fence line, nose buried in her textbook. Suddenly cold fingers latch over her mouth, and she’s pinned against a slippery nylon coat that smells of cigarettes. The textbook slips out of her grasp as she arches her back, bucking against her assailant, even biting fruitlessly at the hand over her mouth. But it’s hopeless- already she can feel the dull ache in her muscles at the strain, something she would never care about until now.

“I have someone who wants to see you, deary,” the voice of her assailant rasps in her ear, and she can feel the tickle of a beard and mustache. It’s only moments before the needle slides into her neck and darkness claims her.

{}{}{}

Sherlock Holmes steps outside into the pouring rain. An inaudible sigh escapes his lips. He strolls under the overhang of  _ Speedy’s _ and pulls out his phone, scrolling to John’s contact.

_ At Speedy’s. Come if convenient. _ Sherlock’s fingers pause over the keys for a moment, and then he adds;  _ If inconvenient, come anyway. -SH _

The response is almost instant.  _ Rosie, Sherlock. -J _

_ Bring Watson if you must. -SH _

_ Coming -J _ Sherlock entered the diner, and was immediately enveloped by Mrs. Hudson.

“Oh, Sherlock dear, do come in! It’s just been awful- all the construction racket and people dredging mud everywhere,” she prattled, setting a cup of tea on a table and pushing Sherlock into a chair. “They’ve only just only opened back up- Speedy’s that is- lucky they didn’t get a lot of damage. Sherlock, I swear if it was one of your experiments-”

“It wasn’t my fault,” Sherlock said dryly, sipping his tea. “It was the bomb.”

Mrs. Hudson huffed. “That’s what you always say, dear. Oh, look, there’s John, better let him in, the poor dear.” John sat down in the chair across from him, hair plastered to his head from the downpour.

“It’s raining-”

“It’s London,” Sherlock interrupted without looking up from his mobile. “Where’s Rosie?”

John shrugged good naturedly. “She started fussing and I couldn’t settle her down, so I handed her off to Molly.”

“Mmm...” Sherlock took one hand away from his typing to sip his tea without looking up. John looked bemused.

“Yes, Molly, the one you confessed your undying love to-”

“Don’t exaggerate, John.” Sherlock clicked a button on the side of his phone, blacking out the screen. “I seem to have found myself without a flat at the moment.”

John looks bemused. Mrs. Hudson shouts something incomprehensible.

“It’s not my fault!” Sherlock bellows in reply, and Mrs. Hudson comes busling out of a back room. 

“If you say so, dear.” She disappears behind the door again.

John sips at his tea. “Well... I’m sure you could bunk at Molly’s.”

Sherlock raised his brows. “God no.”

John frowns. “Why not?”

Sherlock picks up his mobile again. “Because.”

A sigh. “Sherlock…”

Sherlock drains his tea with a disgusted look. “Piss off. Ah, Lestrade has a double homicide for us! Elderly couple locked in the bathroom from the inside and bodies dumped in the tub. Splendid!”

John resisted the urge to roll his eyes. “Just let me text Molly on the way there.”

Something flickered across Sherlock’s normally blank face. “Your coming with me?”

John scoffed. “ ‘Course I am.” And with that, they strode from the little cafe into the storm.


	2. Chapter 2

#  Chapter 2

Lestrade is waiting for them outside beneath the small overhang of a dreary townhouse. The rain had lightened, but the wind has picked up, and Sherlock turning up his insufferably large collar on the coat now has a practical purpose against the rain flying sideways at them. As Sherlock bounded up the steps looking for all the world that he had just won the lottery, Lestrade gruffly approached.

“Sherlock, buddy, I need you to not go bounding in there. I want Anderson to go with you.”

Both John and Sherlock opened their mouths. Lestrade thew up his hands. “Look, it’s not my idea. Your brother-”

Sherlock let out a noise between a growl and a hiss. 

“Yeah, yeah, I know. I just don’t want to mess with higher powers-”

“No, you just want to get laid with my brother,” Sherlock says matter-of-factly. Donavan is gaping like a fish, and Lestrade looks slightly pink.

“Right… um… Anderson- uh, just… get going.” Lestrade made a vague gesture with his hands. 

Sherlock rushes into the house like a hound after a hare. Immediately, he leaps to the stairs. John and Anderson are right behind him-

Anderson curses as Sherlock skids suddenly to a halt. The pale hand clutching the doorframe begins to shake. John shoves his way past Anderson, gun drawn- and stares too.

On the bathroom wall, in written blood, is music. Sherlock’s brain is flying a mile a minute, but his gaze hasn’t even touched the first note. No, it’s the title of the composition-  _ The Station Master. _ Then Sherlock does something he hasn’t done since Serbia-

He bolts. Completely and utterly bolts, tearing though Anderson, Lestrade, the police tape. Everything is completely vividly in focus but blurred at the same time, an HD video playing too fast…

When he finds himself again, he has his back against a cement wall. He feels terrible and jittery like he’s coming down from a cocaine high. A hand brushes his cheek and Sherlock flinches, head cracking against the wall. There’s a quite curse at that, and all at once the tension flees Sherlock’s body.

_ “John.” _ he breathes, and there’s a shaky laugh.

“Yeah, just me, Sherlock.” 

“It’s him.” A quick intake of air.

“Right. Let’s go home.”

{}{}{}

The room was dark, the only light the bluish glow of a television. A silhouette of a man was outlined against it. The VCR audible clicks and wurrs, then begins to play. It’s a tape of a news broadcast.

The reporter, a greying haired man, stands in front of the interviewee, a smartly dressed teenage girl. She’s nervous, and fiddling with something in her hands below the camera’s view.

_ “So, your the daughter of Daneil Jones, is that right?”  _ The reporter is loud and boisterous, and the girl shys away just a little.

_ “Yes, I’m Sophia. But I don’t believe my parents pertain to the matter at hand.”  _ Despite her fear, she spoke loud, enunciating every word. The man watching the tv nodded his head.

_ “But you  _ are _ -”  _ The reporter continued to press, and Sophia scowled.

_ “Please don’t prove yourself as a stereotype, Mr. Fox. I despise stereotypes.”  _ She sniffed. The watcher clapped his hands and grinned in delight.

“Oh, darling, your  _ so _ special.” The tape continued. There’s some hustling, and an older blond woman takes up the mic instead.

_ “So sorry about that, Sophia. Do you mind talking about your actions today?” _ Sophia grinned and stared into the camera.

_ “I won the Poetry Out Loud Competition.” _ The reporter’s smile is motherly. 

_ “Yes, you did fantastic. Is there anything else you like to say?” _ Sophia’s face twists.

_ “A great deal of things, but I won’t. They wouldn’t matter.” _ The reporter frowned.

_ “Why wouldn’t they matter?” _ Sophia looks so old at that moment.

_ “Because that’s the world we live in.” _ The tape cuts to black. The man watching jumps of the chair, smiling. He’s pink hair gleams in the darkness.

“Oh Sherlock,” he sings. “Were going to have  _ so much fun!” _


	3. Chapter 3

#  Chapter 3

The cab is halfway across London before John remembers. There  _ is no _ 221B to go back to. He leans his head back and sighs, rubbing his temples.

The cabby looks at him in the rearview mirror. “Alright?”

“God, I just remembered- could you take us to 1239 Hathingburg Court. Sorry.”

“Fine by me mate. Are you sure your friend doesn't need a hospital?” The cab turns right, and a streetlight glares in John’s eyes, making him squint. They really needed to stop doing midnight cab rides. Sherlock doesn't react at all to the sudden brightness then dark again. He just sitting rigidly straight, as stiff as a board.

“War vet, is he?” the cabby adresses John again.

_ Hmm, it didn’t feel any different- killing the innocent. _

_ I’m going to apply some emotional context now. _

_ Oh, no- the countdown is for me. _

John shakes his head. “Yeah. Sure, yeah.” The cab pulls up to Mary’s house. John turns to Sherlock. Sherlock’s head snaps around, a snarl on his face.

“ _ I’m fine, John.” _ He slams the cab door and whips around, stalking up the cement sidewalk. John turns to the cabby and hands the money.

“Sorry about that.” The cabby shrugs.

“All’s well.” John steps back onto the curb. The cabby pauses for a moment.

“Get him a kid.”

John blinks.  _ “What?” _

The cabby tips his hat. “A kid. It gives people something to live for.” The cab speeds away. John stares. The dose a double take.

The lawn is empty, the living room light is on, and  _ god dammit he did NOT give Sherlock a key- _

“SHERLOCK!”

{}{}{}

The first thing she does before opening her eyes is breaths. Then, eyes still closed, begins to examine the room. A dank, musty smell- it reminded her of her cousin's unused basement. She frowned. That would mean she would have to be outside of her coastal, flood prone city. A worrying thought. She’s tied to a wooden chair with zip ties- arguably the best thing to tie a person up with. Cheap, resistant to water damage, strong enough so you can’t snap it, and in trying to it can break the skin and potentially cut into arteries in the wrists. The wooden chair was a mistake though. Humidity can make the wood swell and shrink, loosening parts and pieces over time. It seemed solid at the moment though, and she didn’t want to push too hard in any one spot and tip over.

Opening her eyes, there wasn’t much else to see. She was seated towards a blank white wall, a tan outlet her only company. There’s something wrong with that outlet. She tentatively goes to kick it-

-a door behind her bangs open. Her heart rate spikes at the heavy footsteps. There’s no warning, and suddenly pain slices across her back, and she lets out a sound between a gasp and a scream. She closes her eyes, brow furrowing.  _ Most likely, all they want is a reaction. I won’t give it to them. But I need an outlet or I won’t last long. _ She new that much about herself. So she sat up straight, squared her shoulders-

-another blow rocks her frame.  _ I can do this. I can survive this.  _

“There will come a soldier, who carries a mighty sword.” Blood pounds in her temples, and her ears ring. Relying on muscle memory, she sings though gasps of pain.

_ Soldier, poet, king. _

_ Soldier, poet, king. _

_ Soldier, poet, king... _


	4. Chapter 4

#  Chapter 4

No one, not even Sherlock himself, will never quite figure out how the grainy footage got to the island prison. But it did. And the third Holmes stares down at it. And for the first time in her life, she let the past go. She shattered the glass again, but for once not for her brother. The world is ending, and there's work to do.

And she will be at the new dawn.

{}{}{}

John sighs deeply, glancing back at the slumped form of Sherlock on the sofa. Running his fingers through his hair with a groan, he clicks on the tv.

“-That was the latest on president Trump. A video was posted and when viral around 2am last night- several countries have banned the video due to it’s graphic and disturbing nature-”

John’s about to change the channel when-

“-reportaly addressed to Sherlock Holmes, the video shows a teenage girl being whipped and raped-” John’s finger slams down on the power button on the remote and whips his head back to see an uncharacteristically pale Sherlock, eyes wide.

“God  _ damnit,  _ Sherlock.”

“It’s not her. It’s not Euros. We had an agreement. I played her game, she saved you.”

John saw red.  _ “She’s a phycopath, Sherlock!” _

Sherlock shook his head forcefully, curls bouncing. “No, it’s not her style. It would be more subtle, not on international news. This is the same person who left the music on the wall.”

John rubbed his eyes. “Damnit, Sherlock. Why does this always happen to us?”

Sherlock shrugged. There’s a moment of silence, then- “John?”

“What?”

“The game’s afoot.”

{}{}{}

A file arrives at the desk of Mycroft Holmes. That file is looked at, frowned upon, and handed off to another minion. The file results in him taking another trip to the island prison.

“Eurus.” he greets her.

“Brother dear.” They stare at each other for a moment, sizing the other up.

“Get on with it, I haven’t got all day.” Eurus paces back in forth in her cell.

“Oh yes you do,” she sings, and Mycroft grits his teeth.

“If all you want is to taunt me, I would be very disappointed.”

Eurus smiles. “Someone’s coming for  _ Sherlock _ .” Mycroft’s blood runs cold. “Oh no, not me. He played my game.”

“Who?”

She pouts. “But I thought you were the British Government, the oh-so-smart-”

_ “Who is coming for Sherlock?!” _ Mycroft’s voice rings out, echoing in the enclosed space. Eurus rolls her eyes.

“Impatient are we, brother dear?” Her face goes blank. “You know who's coming for him. We aren't the only bloodline of geniuses. I’m surprised the British Government hasn't kept a better eye on him.”

Mycroft’s grip on his umbrella tighten’s by a fraction. “Why does he want Sherlock?”

Eurus shrugs. “Sex, revenge, who knows? At the end of the day though, Sherlock isn’t the end goal. He’s not quite as obsessive as his brother. Oh, no, he wants to end the world, Mycroft. And I’ll be there to stand in the ashes.”

Mycroft strides out of the room, barking into an earpiece. 

_ “I want all eyes on Jay Moriarty. Now!” _


	5. Chapter 5

#  Chapter 5

The starch white walls, the dry, recirculated air. The sterile gowns- the first line of protection. Next the powder, then the gloves- it’s all coming back. The thrill, the pure, animalistic  _ danger _ of the pathogens. The rubber smell- almost overwhelming- of the hazmat suit brings a smile to his face.

It’s the door that bars him to Biosafety Level Four that makes him pause. There’s an image- fleeting, but it’s there- of a brown haired stout woman, who had never bowed to anyone- begging and pleading on her knees. He blinks and it’s gone.

When he steps into the lab, he just breathes. The bizarre atmosphere of sterility and filth. Killers contained in polished test tubes. The man emits another crazed grin, and crosses the room to a line of freezers. The particular one he seeks contains filoviruses- some of the deadliest pathogens ever discovered. He opens it.

The names skitter across the surface of his perception- there is only one he seeks. Only one will do. When he finds it, he holds the vial tenderly. It’s quickly replaced by a look alike, then the freezer closes with a snap. Chances are, it will be months before the missing vial is discovered. By then it would be too late.

{}{}{}

It’s John who points it out first. It’s a frustrated, offhand comment after them both staring at the 2 minute clip of video that appeared in Sherlock’s inbox. John was shaking from exhaustion and anger, seeing the whip marks appear on the little girl’s back again and  _ again _ and  _ AGAIN. _

“She looks like you.”

“ _ No she dosen’t,” _ Sherlock immediately snaps at him, but nonetheless fiddles with the software, pausing the footage and clearing up the still. “There see, she looks like my mother!” Sherlock cried triumphantly. John’s about ready to throttle him.

“Your mother who  _ looks like you, _ Sherlock.”

“John, my mother is a mediocre looking woman who-”

“Sherlock.”

“-despite popular belief, looks nothing like me-”

“ _ Sherlock.” _

“-and it is trivial to say that familial relation can be-”

“ _ SHERLOCK! _ Her neck, look.” John waves a finger at the blurry 3 digit number tattooed on her neck. Sherlock frowns. John starts to open his mouth.

“Please don’t say something as trivial as ‘it’s a prison tattoo’, John.” 

“Maybe she’s like that girl from  _ Stranger Things-” _

“John, it is very highly unlikely she was abducted by some secret government project- even if she was, there are numerous more effective ways of identifying test subjects-”

“Maybe she’s a clone or a twin or something. Oh, I bet she’s a clone of you!”

“Your delirious, John. Go to bed.”

John yawned. “Maybe. But I’m not the one saying I don’t look like my own mother.”


	6. Chapter 6

#  Chapter 6

“John.” John groaned and threw the blanket over his head. Immature, yes, but he was done getting up at the crack of dawn for  _ Sherlock bloody Holmes- _

“We have a case, John.” Suddenly the day prior comes flooding back, and his blood runs cold. He opens his eyes to a fully dressed Sherlock. He squints.

“Mycroft’s coming,” Sherlock sniffs to Johns unanswered question. John frowns and decides not to ask how he knows.

“Good. Your learning.” 

“Bugger off.”

When John comes down the stairs a few minutes later, Sherlock is glaring at the door to the flat like its done a dishonor on his family. John sighs and tries to find a  _ not  _ moldy piece of bread.

“Sherlock, If you need to do mold experiments, please go out and buy your own-”

“You were right.” Sherlock says in a low tone that John’s never quite heard before. “She looks like me.”

John looks up from rummaging through a drawer, visibly puzzled. “What?”

“You said, at 2:37 this morning, that-”

“I know what I said. It was also  _ two in the morning.” _ John says exasperated. “You said it yourself- I was tired.”

Sherlock scowls, a gesture so familiar that John can almost ignore the tickle in the back of his mind that  _ something's not right. _

“Well, I re-evaluated.” John manages to find the toaster.

“It’s nice you’ve finally taken something to heart, I guess. So?”

He’s ment with silence. John frowns at the toster, which is making a rattling sound. “Go on- I know I’m going to hear it anyway.”

More silence. “Sherlock?” John turns on his heal slowly towards the living room. Sherlock’s lips are stretched into a thin line, and he’s staring down at his hands. Their shaking.

“Mycroft’s bringing over the files.” John takes a cautious step closer.

“Sherlock…”

“Your right John, dammit. You're always right.” A tear falls from Sherlock’s right eye. Alarmed, John tentatively crouches beside Sherlock’s leather armchair. They had been in an odd sort of limbo since Sherringford. ‘It is what it is’ didn’t seem to cut it anymore. John knew one of them was going to break, and he hoped and prayed it wouldn’t be Sherlock. Because despite all his friendships, his relationship with Mary, raising his daughter… none of them would ever come close to what he had with Sherlock.

He had already spent two long years seeing what he became without Sherlock.

Never again.

But despite being his best friend, Sherlock was  _ Sherlock _ , and John was  _ just John. _ And he didn’t know what to do. So he talked.

He talked about cases from medical journals, the cases at the clinic, the heat wave in America. He talked, and slowly, Sherlock came back to life. John knew that the way Sherlock had hugged him after Mary’s death could never provide the same comfort as it did John. But he could give information, facts to latch onto, the same way physical contact would steady any other person. Soon Sherlock was nodding along with John’s monologue, fingers steepled and eyes closed.

“John?”

“Yes?”

“Do you think Mycroft would lie to me?”

John frowns. “I don’t know. If it was to protect you, maybe.”

Sherlock snorts and opens his eyes. “Sentiment, John? From Myrcroft?” But those words rang false after Sherringford, and Sherlock knew that. “During his time at University, Mycroft applied some of Mummy’s formulas to make the most accurate facial scanning software to date.”

John raised his eyebrows. Sherlock smirks.

“He always said it was for the end of term assignment. Doubtful. I of course, hacked into his computer immediately and downloaded it.”

John shakes his head again, imagining what chaos the Holmes household must have been growing up.

“It’s still remains in my possession today. I never used it until last night, and I must say the interface is horrible.”

“Only because you ruined it.” John’s head whips around to see an open door and a Mycroft Holmes. The oldest Holmes sibling smoothly pulls out a manila folder, which Sherlock snatches up like a starving dog given a bone.

“I have a case for you, brother.” Sherlock is thumbing through the pages, brow furrowed. Mycroft places a hand on the folder to stop the furious flipping of pages, and Sherlock looks up at him, surprised.

“A moment of your time, brother dear,” Mycroft says softly, and Sherlock slowly closes the file. John’s eyebrows nearly touch his hair.

“Recently, a high profile retired American army colonel, Nancy Jaax, was brutally murdered and her body was strung up on top of a flagpole in her former workplace. I’m sure you know what she was famous for, Doctor Watson.”

John swallows. “Ebola.”

Mycroft nods. “Yes. Understandably, the FBI and CIA want to know how Jaax’s blood ended up in a crime scene as a musical composition in London.” John’s mouth falls open.

“Get to it, Mycroft, stop stating the obvious,” Sherlock growled. “How does the girl fit in?”

“I suspect it’s to simply keep you out of the way of his plans, brother dear. Now, the doctor looks horrible confused over there, brother, why don’t you remedy that?”

Sherlock runs his finger through his hair. “The station master, John. I don’t know why we didn’t pay more attention. In the hours I spent examining Moriarty’s evey miniscule movement and breath, I  _ forgot,  _ John.”

John’s throat went dry. “Moriarty’s brother.”

“ _ Yes,  _ John! And he  _ knows _ he has to get me out of the way!” Sherlock shoves the manila folder at John’s chest, a black and white CCTV image of an unblemished and unharmed girl on top. The same one from the video they spent the night before pouring over. And the name on the file is like a punch to the gut.

_ Sophia Holmes. _

“Baskerville, John!  _ Baskerville! _ _ They told us! _ ” Sherlock springs from his chair, pacing. 

“Told us what?” John asks faintly.

“Cloning, John!  _ Human cloning! _ Oh, John, this man- he might be even better stimulation then his brother, John-”

“A clone of  _ you, _ Sherlock?” John manages to wheeze out. Sherlock rolls his eyes.

“Yes, John, were past that- not he’s trying to destroy the world with the  _ Ebola Zaire _ virus! The man is  _ insane, _ John!” Sherlock looks giddy.

John’s head is spinning. He stumbles to the door. “Rosie, she’s been at Molly’s since 3 yesterday,” he manages to sputter out before shoving past the two Holmes brothers and flying down the stairs into the fall chill.

**Notes for the Chapter:**

> For context: The events of this story so far have happened in less than a 48 hour period. The only exception is the first scene with the initial kidnapping. That takes place about a week and a half prior to the rest of the story. The timeline might seem slightly confusing, so I wanted to clarify.


End file.
